sgkit
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sgkit-dev
Scalable genetics toolkit
When I run the pc_relate on my dataset, it gives an error "Input must be a square matrix to perform lu decomposition" in line 157 (half_beta = da.linalg.inv(2 * r).dot(q.T).dot(imputed_call_g.T))....
@eric-czech mentioned on a [recent developer call](https://github.com/pystatgen/sgkit/discussions/553) that we use Numba rather than CuPy to target GPUs because CuPy does not have masked array support https://github.com/cupy/cupy/issues/2225.
Demonstrating GPU cost efficiency and progressing on issues raised in https://github.com/pystatgen/sgkit/issues/390 may both be aided by creating a representative public workflow for UKB GWAS. A single notebook that executes a...
When I run the HWE function on the simulated dataset or my own dataset, I get > Traceback (most recent call last): File "", line 1, in File "/home/ubuntu/anaconda3/lib/python3.7/site-packages/sgkit/stats/hwe.py", line...
In the following code the dask version is returning ints in [0, 2] and the numpy arrays are floats in [0, 1]. https://github.com/pystatgen/sgkit/blob/9cc4490d89c27d5e00322b517a74c626043b105d/sgkit/tests/test_distance.py#L20-L28 Following change was suggested for the same...
I currently have the testing VCF file, but the number of alleles is 4. Do you have any dataset with alleles as 2? Or do we have functions, (like filter...
We use Literal types for creating a list of Enum string values to be used in the code base, but we only rely on mypy at the moment for checking...
Chris Chang recently published a [protocol](https://link.springer.com/protocol/10.1007/978-1-0716-0199-0_3) for PLINK with instructions on how to perform common data management operations. It might be useful to bring this protocol over to our documentation...
We'll soon have some GPU implementation of Pairwise distance functionality: https://github.com/pystatgen/sgkit/pull/498 ## Primer on GPU and the Problem The architecture of a GPU is divided into grids and each grid...
Long story short, the problematic line in our code is: https://github.com/pystatgen/sgkit/blob/41827f3fd116d59ab4dc8b119a15ad5f3be730b9/sgkit/stats/regenie.py#L364 https://github.com/dask/dask/pull/6748 is a special case optimisation: > When the slow-moving (early) axes in .reshape are all size 1 Our...
